1
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Gurdon B, Yates SC, Csucs G, Groeneboom NE, Hadad N, Telpoukhovskaia M, Ouellette A, Ouellette T, O'Connell KMS, Singh S, Murdy TJ, Merchant E, Bjerke I, Kleven H, Schlegel U, Leergaard TB, Puchades MA, Bjaalie JG, Kaczorowski CC. Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model. Commun Biol 2024; 7:605. [PMID: 38769398 PMCID: PMC11106287 DOI: 10.1038/s42003-024-06242-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Alzheimer's disease (AD) is broadly characterized by neurodegeneration, pathology accumulation, and cognitive decline. There is considerable variation in the progression of clinical symptoms and pathology in humans, highlighting the importance of genetic diversity in the study of AD. To address this, we analyze cell composition and amyloid-beta deposition of 6- and 14-month-old AD-BXD mouse brains. We utilize the analytical QUINT workflow- a suite of software designed to support atlas-based quantification, which we expand to deliver a highly effective method for registering and quantifying cell and pathology changes in diverse disease models. In applying the expanded QUINT workflow, we quantify near-global age-related increases in microglia, astrocytes, and amyloid-beta, and we identify strain-specific regional variation in neuron load. To understand how individual differences in cell composition affect the interpretation of bulk gene expression in AD, we combine hippocampal immunohistochemistry analyses with bulk RNA-sequencing data. This approach allows us to categorize genes whose expression changes in response to AD in a cell and/or pathology load-dependent manner. Ultimately, our study demonstrates the use of the QUINT workflow to standardize the quantification of immunohistochemistry data in diverse mice, - providing valuable insights into regional variation in cellular load and amyloid deposition in the AD-BXD model.
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Affiliation(s)
- Brianna Gurdon
- The Jackson Laboratory, Bar Harbor, ME, USA
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA
| | - Sharon C Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gergely Csucs
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nicolaas E Groeneboom
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Niran Hadad
- The Jackson Laboratory, Bar Harbor, ME, USA
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Andrew Ouellette
- The Jackson Laboratory, Bar Harbor, ME, USA
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA
| | - Tionna Ouellette
- The Jackson Laboratory, Bar Harbor, ME, USA
- Tufts University Graduate School of Biomedical Sciences, Medford, MA, USA
| | - Kristen M S O'Connell
- The Jackson Laboratory, Bar Harbor, ME, USA
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA
- Tufts University Graduate School of Biomedical Sciences, Medford, MA, USA
| | - Surjeet Singh
- The Jackson Laboratory, Bar Harbor, ME, USA
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Ingvild Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Heidi Kleven
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ulrike Schlegel
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A Puchades
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
| | - Catherine C Kaczorowski
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA.
- Tufts University Graduate School of Biomedical Sciences, Medford, MA, USA.
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
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2
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Dey P, Rajalaxmi S, Saha P, Thakur PS, Hashmi MA, Lal H, Saini N, Singh N, Ramanathan A. Cold-shock proteome of myoblasts reveals role of RBM3 in promotion of mitochondrial metabolism and myoblast differentiation. Commun Biol 2024; 7:515. [PMID: 38688991 PMCID: PMC11061143 DOI: 10.1038/s42003-024-06196-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Adaptation to hypothermia is important for skeletal muscle cells under physiological stress and is used for therapeutic hypothermia (mild hypothermia at 32 °C). We show that hypothermic preconditioning at 32 °C for 72 hours improves the differentiation of skeletal muscle myoblasts using both C2C12 and primary myoblasts isolated from 3 month and 18-month-old mice. We analyzed the cold-shock proteome of myoblasts exposed to hypothermia (32 °C for 6 and 48 h) and identified significant changes in pathways related to RNA processing and central carbon, fatty acid, and redox metabolism. The analysis revealed that levels of the cold-shock protein RBM3, an RNA-binding protein, increases with both acute and chronic exposure to hypothermic stress, and is necessary for the enhanced differentiation and maintenance of mitochondrial metabolism. We also show that overexpression of RBM3 at 37 °C is sufficient to promote mitochondrial metabolism, cellular proliferation, and differentiation of C2C12 and primary myoblasts. Proteomic analysis of C2C12 myoblasts overexpressing RBM3 show significant enrichment of pathways involved in fatty acid metabolism, RNA metabolism and the electron transport chain. Overall, we show that the cold-shock protein RBM3 is a critical factor that can be used for controlling the metabolic network of myoblasts.
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Affiliation(s)
- Paulami Dey
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
- SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Srujanika Rajalaxmi
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Pushpita Saha
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Purvi Singh Thakur
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Maroof Athar Hashmi
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Heera Lal
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Nistha Saini
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Nirpendra Singh
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India
| | - Arvind Ramanathan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK-Post, Bellary Rd, Bengaluru, 560065, Karnataka, India.
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3
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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4
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Li L, Han J, Lo HYG, Tam WWL, Jia H, Tse ECM, Taliaferro JM, Li Y. Symmetry-breaking malachite green as a near-infrared light-activated fluorogenic photosensitizer for RNA proximity labeling. Nucleic Acids Res 2024; 52:e36. [PMID: 38407347 DOI: 10.1093/nar/gkae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/27/2024] Open
Abstract
Cellular RNA is asymmetrically distributed in cells and the regulation of RNA localization is crucial for proper cellular functions. However, limited chemical tools are available to capture dynamic RNA localization in complex biological systems with high spatiotemporal resolution. Here, we developed a new method for RNA proximity labeling activated by near-infrared (NIR) light, which holds the potential for deep penetration. Our method, termed FAP-seq, utilizes a genetically encoded fluorogen activating protein (FAP) that selectively binds to a set of substrates known as malachite green (MG). FAP binding restricts the rotation of MG and rapidly activates its fluorescence in a wash-free manner. By introducing a monoiodo modification to MG, we created a photosensitizer (MG-HI) with the highest singlet oxygen generation ability among various MG derivatives, enabling both protein and RNA proximity labeling in live cells. New insights are provided in the transcriptome analysis with FAP-seq, while a deeper understanding of the symmetry-breaking structural arrangement of FAP-MG-HI was obtained through molecular dynamics simulations. Overall, our wash-free and NIR light-inducible RNA proximity labeling method (FAP-seq) offers a powerful and versatile approach for investigating complex mechanisms underlying RNA-related biological processes.
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Affiliation(s)
- Lan Li
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Jinghua Han
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Hei-Yong G Lo
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Winnie Wai Ling Tam
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories, Hong Kong 999077, China
| | - Han Jia
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Edmund Chun Ming Tse
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories, Hong Kong 999077, China
- CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Hong Kong 999077, China
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ying Li
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories, Hong Kong 999077, China
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5
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Pang D, Yu Y, Zhao B, Huang J, Cui Y, Li T, Li C, Shang H. The Long Non-Coding RNA NR3C2-8:1 Promotes p53-Mediated Apoptosis through the miR-129-5p/USP10 Axis in Amyotrophic Lateral Sclerosis. Mol Neurobiol 2024:10.1007/s12035-024-04059-x. [PMID: 38388775 DOI: 10.1007/s12035-024-04059-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Motor neuron degeneration in amyotrophic lateral sclerosis (ALS) is a form of apoptosis, but the mechanisms underlying this neuronal cell death remain unclear. Numerous studies demonstrate abnormally elevated and active p53 in the central nervous system of ALS patients. Activation of p53-regulated pro-apoptotic signaling pathways may trigger motor neuron death. We previously reported decreased expression of the long non-coding RNA NR3C2-8:1 (Lnc-NR3C) in leukocytes of ALS patients. Here, we show lnc-NR3C promotes p53-mediated cell death in ALS by upregulating USP10 and promoting lnc-NR3C-triggered p53 activation, resulting in cell death. Conversely, lnc-NR3C knockdown inhibited USP10-triggered p53 activation, thereby protecting cells against oxidative stress. As a competitive endogenous RNA, lnc-NR3C competitively binds miR-129-5p, regulating the usp10/p53 axis. Elucidating the link between Lnc-NR3C and the USP10/p53 axis in an ALS cell model reveals a role for long non-coding RNAs in activating apoptosis. This provides new therapeutic opportunities in ALS.
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Affiliation(s)
- Dejiang Pang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Yujiao Yu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Bi Zhao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Jingxuan Huang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Yiyuan Cui
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Tengfei Li
- Department of Neurosurgery, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China.
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China.
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6
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Chauvier A, Walter NG. Regulation of bacterial gene expression by non-coding RNA: It is all about time! Cell Chem Biol 2024; 31:71-85. [PMID: 38211587 DOI: 10.1016/j.chembiol.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
Commensal and pathogenic bacteria continuously evolve to survive in diverse ecological niches by efficiently coordinating gene expression levels in their ever-changing environments. Regulation through the RNA transcript itself offers a faster and more cost-effective way to adapt than protein-based mechanisms and can be leveraged for diagnostic or antimicrobial purposes. However, RNA can fold into numerous intricate, not always functional structures that both expand and obscure the plethora of roles that regulatory RNAs serve within the cell. Here, we review the current knowledge of bacterial non-coding RNAs in relation to their folding pathways and interactions. We posit that co-transcriptional folding of these transcripts ultimately dictates their downstream functions. Elucidating the spatiotemporal folding of non-coding RNAs during transcription therefore provides invaluable insights into bacterial pathogeneses and predictive disease diagnostics. Finally, we discuss the implications of co-transcriptional folding andapplications of RNAs for therapeutics and drug targets.
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Affiliation(s)
- Adrien Chauvier
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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7
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Chen L, Zhang S, Liu S, Gao S. Amyotrophic Lateral Sclerosis Mechanism: Insights from the Caenorhabditis elegans Models. Cells 2024; 13:99. [PMID: 38201303 PMCID: PMC10778397 DOI: 10.3390/cells13010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a debilitating neurodegenerative condition characterized by the progressive degeneration of motor neurons. Despite extensive research in various model animals, the cellular signal mechanisms of ALS remain elusive, impeding the development of efficacious treatments. Among these models, a well-characterized and diminutive organism, Caenorhabditis elegans (C. elegans), has emerged as a potent tool for investigating the molecular and cellular dimensions of ALS pathogenesis. This review summarizes the contributions of C. elegans models to our comprehension of ALS, emphasizing pivotal findings pertaining to genetics, protein aggregation, cellular pathways, and potential therapeutic strategies. We analyze both the merits and constraints of the C. elegans system in the realm of ALS research and point towards future investigations that could bridge the chasm between C. elegans foundational discoveries and clinical applications.
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Affiliation(s)
| | | | | | - Shangbang Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (L.C.); (S.Z.); (S.L.)
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8
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Yim MK, Stuart CJ, Pond MI, van Hoof A, Johnson SJ. Conserved Residues at the Mtr4 C-Terminus Coordinate Helicase Activity and Exosome Interactions. Biochemistry 2024; 63:159-170. [PMID: 38085597 PMCID: PMC10984559 DOI: 10.1021/acs.biochem.3c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Mtr4 is an essential RNA helicase involved in nuclear RNA processing and degradation and is a member of the Ski2-like helicase family. Ski2-like helicases share a common core architecture that includes two RecA-like domains, a winged helix, and a helical bundle (HB) domain. In Mtr4, a short C-terminal tail immediately follows the HB domain and is positioned at the interface of the RecA-like domains. The tail ends with a SLYΦ sequence motif that is highly conserved in a subset of Ski2-like helicases. Here, we show that this sequence is critical for Mtr4 function. Mutations in the C-terminus result in decreased RNA unwinding activity. Mtr4 is a key activator of the RNA exosome complex, and mutations in the SLYΦ motif produce a slow growth phenotype when combined with a partial exosome defect in S. cerevisiae, suggesting an important role of the C-terminus of Mtr4 and the RNA exosome. We further demonstrate that C-terminal mutations impair RNA degradation activity by the major RNA exosome nuclease Rrp44 in vitro. These data demonstrate a role for the Mtr4 C-terminus in regulating helicase activity and coordinating Mtr4-exosome interactions.
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Affiliation(s)
- Matthew K. Yim
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322, USA
| | - Catherine J. Stuart
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Markell I. Pond
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322, USA
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9
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Mir FA, Amanullah A, Jain BP, Hyderi Z, Gautam A. Neuroepigenetics of ageing and neurodegeneration-associated dementia: An updated review. Ageing Res Rev 2023; 91:102067. [PMID: 37689143 DOI: 10.1016/j.arr.2023.102067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Gene expression is tremendously altered in the brain during memory acquisition, recall, and forgetfulness. However, non-genetic factors, including environmental elements, epigenetic changes, and lifestyle, have grabbed significant attention in recent years regarding the etiology of neurodegenerative diseases (NDD) and age-associated dementia. Epigenetic modifications are essential in regulating gene expression in all living organisms in a DNA sequence-independent manner. The genes implicated in ageing and NDD-related memory disorders are epigenetically regulated by processes such as DNA methylation, histone acetylation as well as messenger RNA editing machinery. The physiological and optimal state of the epigenome, especially within the CNS of humans, plays an intricate role in helping us adjust to the changing environment, and alterations in it cause many brain disorders, but the mechanisms behind it still need to be well understood. When fully understood, these epigenetic landscapes could act as vital targets for pharmacogenetic rescue strategies for treating several diseases, including neurodegeneration- and age-induced dementia. Keeping this objective in mind, this updated review summarises the epigenetic changes associated with age and neurodegeneration-associated dementia.
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Affiliation(s)
- Fayaz Ahmad Mir
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Zeeshan Hyderi
- Department of Biotechnology, Alagappa University, Karaikudi, India
| | - Akash Gautam
- Centre for Neural and Cognitive Sciences, University of Hyderabad, Hyderabad, India.
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10
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Saha D, Dhyani V, Giri L. In vitro laser scanning confocal microscopy and unsupervised segmentation: Quantification of cytosolic calcium and RNA distribution in hypoxic neurons. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38083364 DOI: 10.1109/embc40787.2023.10340952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The mimicry of neurodegenerative diseases in vitro can be observed through the induction of chronic hypoxia, and the impact of this stress is monitored using multiplexed imaging techniques. While laser scanning confocal microscopy (LSCM) is a valuable tool for observing single neurons under degenerative conditions, accurately quantifying RNA distribution and cell size by deep learning tools remains challenging due to the lack of annotated training datasets. To address this, we propose a framework that combines 3D tracking of RNA distribution and cell size identification using unsupervised image segmentation. Additionally, we quantified the calcium level in neurons using fluorescent microscopy using unsupervised image segmentation. First, we performed imaging of neuronal morphology using differential interference contrast (DIC) optics and RNA/calcium level imaging using fluorescent microscopy. Next, we performed k-means clustering-based cell segmentation. The results show that our framework can distinguish between distinct neuronal states under control and chronic hypoxic conditions. The analysis reveals that hypoxia induces a significant increase in cytosolic calcium level, reduction in neuron diameter, and alterations in RNA distribution.Clinical Relevance- The proposed framework is crucial to study the neurodegeneration process and evaluating the efficacy of neuroprotective drugs through image analysis.
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11
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Morelli KH, Smargon AA, Yeo GW. Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders. RNA (NEW YORK, N.Y.) 2023; 29:489-497. [PMID: 36693761 PMCID: PMC10019361 DOI: 10.1261/rna.079519.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Disruptions in RNA processing play critical roles in the pathogenesis of neurological diseases. In this Perspective, we discuss recent progress in the development of RNA-targeting therapeutic modalities. We focus on progress, limitations, and opportunities in a new generation of therapies engineered from RNA binding proteins and other endogenous RNA regulatory macromolecules to treat human neurological disorders.
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Affiliation(s)
- Kathryn H Morelli
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
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12
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Santiago JA, Quinn JP, Potashkin JA. Co-Expression Network Analysis Identifies Molecular Determinants of Loneliness Associated with Neuropsychiatric and Neurodegenerative Diseases. Int J Mol Sci 2023; 24:ijms24065909. [PMID: 36982982 PMCID: PMC10058494 DOI: 10.3390/ijms24065909] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/06/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Loneliness and social isolation are detrimental to mental health and may lead to cognitive impairment and neurodegeneration. Although several molecular signatures of loneliness have been identified, the molecular mechanisms by which loneliness impacts the brain remain elusive. Here, we performed a bioinformatics approach to untangle the molecular underpinnings associated with loneliness. Co-expression network analysis identified molecular 'switches' responsible for dramatic transcriptional changes in the nucleus accumbens of individuals with known loneliness. Loneliness-related switch genes were enriched in cell cycle, cancer, TGF-β, FOXO, and PI3K-AKT signaling pathways. Analysis stratified by sex identified switch genes in males with chronic loneliness. Male-specific switch genes were enriched in infection, innate immunity, and cancer-related pathways. Correlation analysis revealed that loneliness-related switch genes significantly overlapped with 82% and 68% of human studies on Alzheimer's (AD) and Parkinson's diseases (PD), respectively, in gene expression databases. Loneliness-related switch genes, BCAM, NECTIN2, NPAS3, RBM38, PELI1, DPP10, and ASGR2, have been identified as genetic risk factors for AD. Likewise, switch genes HLA-DRB5, ALDOA, and GPNMB are known genetic loci in PD. Similarly, loneliness-related switch genes overlapped in 70% and 64% of human studies on major depressive disorder and schizophrenia, respectively. Nine switch genes, HLA-DRB5, ARHGAP15, COL4A1, RBM38, DMD, LGALS3BP, WSCD2, CYTH4, and CNTRL, overlapped with known genetic variants in depression. Seven switch genes, NPAS3, ARHGAP15, LGALS3BP, DPP10, SMYD3, CPXCR1, and HLA-DRB5 were associated with known risk factors for schizophrenia. Collectively, we identified molecular determinants of loneliness and dysregulated pathways in the brain of non-demented adults. The association of switch genes with known risk factors for neuropsychiatric and neurodegenerative diseases provides a molecular explanation for the observed prevalence of these diseases among lonely individuals.
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Affiliation(s)
| | | | - Judith A Potashkin
- Center for Neurodegenerative Diseases and Therapeutics, Cellular and Molecular Pharmacology Department, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
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13
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Gurdon B, Yates SC, Csucs G, Groeneboom NE, Hadad N, Telpoukhovskaia M, Ouellette A, Ouellette T, O'Connell K, Singh S, Murdy T, Merchant E, Bjerke I, Kleven H, Schlegel U, Leergaard TB, Puchades MA, Bjaalie JG, Kaczorowski CC. Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530226. [PMID: 36909528 PMCID: PMC10002670 DOI: 10.1101/2023.02.27.530226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Alzheimer's disease (AD) is characterized by neurodegeneration, pathology accumulation, and progressive cognitive decline. There is significant variation in age at onset and severity of symptoms highlighting the importance of genetic diversity in the study of AD. To address this, we analyzed cell and pathology composition of 6- and 14-month-old AD-BXD mouse brains using the semi-automated workflow (QUINT); which we expanded to allow for nonlinear refinement of brain atlas-registration, and quality control assessment of atlas-registration and brain section integrity. Near global age-related increases in microglia, astrocyte, and amyloid-beta accumulation were measured, while regional variation in neuron load existed among strains. Furthermore, hippocampal immunohistochemistry analyses were combined with bulk RNA-sequencing results to demonstrate the relationship between cell composition and gene expression. Overall, the additional functionality of the QUINT workflow delivers a highly effective method for registering and quantifying cell and pathology changes in diverse disease models.
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Affiliation(s)
- Brianna Gurdon
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
| | - Sharon C Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gergely Csucs
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nicolaas E Groeneboom
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | | | - Andrew Ouellette
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
| | - Tionna Ouellette
- The Jackson Laboratory, Bar Harbor, ME
- Tufts University Graduate School of Biomedical Sciences, Medford, MA
| | - Kristen O'Connell
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
- Tufts University Graduate School of Biomedical Sciences, Medford, MA
| | | | - Tom Murdy
- The Jackson Laboratory, Bar Harbor, ME
| | | | - Ingvild Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Heidi Kleven
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ulrike Schlegel
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A Puchades
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Catherine C Kaczorowski
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
- Tufts University Graduate School of Biomedical Sciences, Medford, MA
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14
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Sekulovski S, Trowitzsch S. What connects splicing of transfer RNA precursor molecules with pontocerebellar hypoplasia? Bioessays 2023; 45:e2200130. [PMID: 36517085 DOI: 10.1002/bies.202200130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 01/19/2023]
Abstract
Transfer RNAs (tRNAs) represent the most abundant class of RNA molecules in the cell and are key players during protein synthesis and cellular homeostasis. Aberrations in the extensive tRNA biogenesis pathways lead to severe neurological disorders in humans. Mutations in the tRNA splicing endonuclease (TSEN) and its associated RNA kinase cleavage factor polyribonucleotide kinase subunit 1 (CLP1) cause pontocerebellar hypoplasia (PCH), a heterogeneous group of neurodegenerative disorders, that manifest as underdevelopment of specific brain regions typically accompanied by microcephaly, profound motor impairments, and child mortality. Recently, we demonstrated that mutations leading to specific PCH subtypes destabilize TSEN in vitro and cause imbalances of immature to mature tRNA ratios in patient-derived cells. However, how tRNA processing defects translate to disease on a systems level has not been understood. Recent findings suggested that other cellular processes may be affected by mutations in TSEN/CLP1 and obscure the molecular mechanisms of PCH emergence. Here, we review PCH disease models linked to the TSEN/CLP1 machinery and discuss future directions to study neuropathogenesis.
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Affiliation(s)
- Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
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15
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Okamoto J, Wang L, Yin X, Luca F, Pique-Regi R, Helms A, Im HK, Morrison J, Wen X. Probabilistic integration of transcriptome-wide association studies and colocalization analysis identifies key molecular pathways of complex traits. Am J Hum Genet 2023; 110:44-57. [PMID: 36608684 PMCID: PMC9892769 DOI: 10.1016/j.ajhg.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/06/2022] [Indexed: 01/07/2023] Open
Abstract
Integrative genetic association methods have shown great promise in post-GWAS (genome-wide association study) analyses, in which one of the most challenging tasks is identifying putative causal genes and uncovering molecular mechanisms of complex traits. Recent studies suggest that prevailing computational approaches, including transcriptome-wide association studies (TWASs) and colocalization analysis, are individually imperfect, but their joint usage can yield robust and powerful inference results. This paper presents INTACT, a computational framework to integrate probabilistic evidence from these distinct types of analyses and implicate putative causal genes. This procedure is flexible and can work with a wide range of existing integrative analysis approaches. It has the unique ability to quantify the uncertainty of implicated genes, enabling rigorous control of false-positive discoveries. Taking advantage of this highly desirable feature, we further propose an efficient algorithm, INTACT-GSE, for gene set enrichment analysis based on the integrated probabilistic evidence. We examine the proposed computational methods and illustrate their improved performance over the existing approaches through simulation studies. We apply the proposed methods to analyze the multi-tissue eQTL data from the GTEx project and eight large-scale complex- and molecular-trait GWAS datasets from multiple consortia and the UK Biobank. Overall, we find that the proposed methods markedly improve the existing putative gene implication methods and are particularly advantageous in evaluating and identifying key gene sets and biological pathways underlying complex traits.
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Affiliation(s)
- Jeffrey Okamoto
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Lijia Wang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xianyong Yin
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Adam Helms
- University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jean Morrison
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.
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16
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Vasiliev GV, Ovchinnikov VY, Lisachev PD, Bondar NP, Grinkevich LN. The Expression of miRNAs Involved in Long-Term Memory Formation in the CNS of the Mollusk Helix lucorum. Int J Mol Sci 2022; 24:ijms24010301. [PMID: 36613744 PMCID: PMC9820140 DOI: 10.3390/ijms24010301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Mollusks are unique animals with a relatively simple central nervous system (CNS) containing giant neurons with identified functions. With such simple CNS, mollusks yet display sufficiently complex behavior, thus ideal for various studies of behavioral processes, including long-term memory (LTM) formation. For our research, we use the formation of the fear avoidance reflex in the terrestrial mollusk Helix lucorum as a learning model. We have shown previously that LTM formation in Helix requires epigenetic modifications of histones leading to both activation and inactivation of the specific genes. It is known that microRNAs (miRNAs) negatively regulate the expression of genes; however, the role of miRNAs in behavioral regulation has been poorly investigated. Currently, there is no miRNAs sequencing data being published on Helix lucorum, which makes it impossible to investigate the role of miRNAs in the memory formation of this mollusk. In this study, we have performed sequencing and comparative bioinformatics analysis of the miRNAs from the CNS of Helix lucorum. We have identified 95 different microRNAs, including microRNAs belonging to the MIR-9, MIR-10, MIR-22, MIR-124, MIR-137, and MIR-153 families, known to be involved in various CNS processes of vertebrates and other species, particularly, in the fear behavior and LTM. We have shown that in the CNS of Helix lucorum MIR-10 family (26 miRNAs) is the most representative one, including Hlu-Mir-10-S5-5p and Hlu-Mir-10-S9-5p as top hits. Moreover, we have shown the involvement of the MIR-10 family in LTM formation in Helix. The expression of 17 representatives of MIR-10 differentially changes during different periods of LTM consolidation in the CNS of Helix. In addition, using comparative analysis of microRNA expression upon learning in normal snails and snails with deficient learning abilities with dysfunction of the serotonergic system, we identified a number of microRNAs from several families, including MIR-10, which expression changes only in normal animals. The obtained data can be used for further fundamental and applied behavioral research.
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Affiliation(s)
- Gennady V. Vasiliev
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Vladimir Y. Ovchinnikov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Pavel D. Lisachev
- Federal Research Center for Information and Computational Technologies, 6 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Natalia P. Bondar
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Larisa N. Grinkevich
- The Federal State Budget Scientific Institution Pavlov Institute of Physiology, Russian Academy of Sciences, 6 nab. Makarova, St. Petersburg 199034, Russia
- Correspondence:
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17
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Current Diagnostic Methods and Non-Coding RNAs as Possible Biomarkers in Huntington’s Disease. Genes (Basel) 2022; 13:genes13112017. [PMID: 36360254 PMCID: PMC9689996 DOI: 10.3390/genes13112017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Whether as a cause or a symptom, RNA transcription is recurrently altered in pathologic conditions. This is also true for non-coding RNAs, with regulatory functions in a variety of processes such as differentiation, cell identity and metabolism. In line with their increasingly recognized roles in cellular pathways, RNAs are also currently evaluated as possible disease biomarkers. They could be informative not only to follow disease progression and assess treatment efficacy in clinics, but also to aid in the development of new therapeutic approaches. This is especially important for neurological and genetic disorders, where the administration of appropriate treatment during the disease prodromal stage could significantly delay, if not halt, disease progression. In this review we focus on the current status of biomarkers in Huntington’s Disease (HD), a fatal hereditary and degenerative disease condition. First, we revise the sources and type of wet biomarkers currently in use. Then, we explore the feasibility of different RNA types (miRNA, ncRNA, circRNA) as possible biomarker candidates, discussing potential advantages, disadvantages, sources of origin and the ongoing investigations on this topic.
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18
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Ly S, Didiot MC, Ferguson CM, Coles AH, Miller R, Chase K, Echeverria D, Wang F, Sadri-Vakili G, Aronin N, Khvorova A. Mutant huntingtin messenger RNA forms neuronal nuclear clusters in rodent and human brains. Brain Commun 2022; 4:fcac248. [PMID: 36458209 PMCID: PMC9707646 DOI: 10.1093/braincomms/fcac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/14/2022] [Accepted: 10/12/2022] [Indexed: 01/25/2023] Open
Abstract
Mutant messenger RNA (mRNA) and protein contribute to the clinical manifestation of many repeat-associated neurological disorders, with the presence of nuclear RNA clusters being a common pathological feature. Yet, investigations into Huntington's disease-caused by a CAG repeat expansion in exon 1 of the huntingtin (HTT) gene-have primarily focused on toxic protein gain-of-function as the primary disease-causing feature. To date, mutant HTT mRNA has not been identified as an in vivo hallmark of Huntington's disease. Here, we report that, in two Huntington's disease mouse models (YAC128 and BACHD-97Q-ΔN17), mutant HTT mRNA is retained in the nucleus. Widespread formation of large mRNA clusters (∼0.6-5 µm3) occurred in 50-75% of striatal and cortical neurons. Cluster formation was independent of age and driven by expanded repeats. Clusters associate with chromosomal transcriptional sites and quantitatively co-localize with the aberrantly processed N-terminal exon 1-intron 1 mRNA isoform, HTT1a. HTT1a mRNA clusters are observed in a subset of neurons from human Huntington's disease post-mortem brain and are likely caused by somatic expansion of repeats. In YAC128 mice, clusters, but not individual HTT mRNA, are resistant to antisense oligonucleotide treatment. Our findings identify mutant HTT/HTT1a mRNA clustering as an early, robust molecular signature of Huntington's disease, providing in vivo evidence that Huntington's disease is a repeat expansion disease with mRNA involvement.
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Affiliation(s)
| | | | | | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kathryn Chase
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Feng Wang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Ghazaleh Sadri-Vakili
- Mass General Institute for Neurodegenerative Disease, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Neil Aronin
- Correspondence may also be addressed to: Neil Aronin 368 Plantation Street, Albert Sherman Center Worcester, MA 01655, USA. E-mail:
| | - Anastasia Khvorova
- Correspondence to: Anastasia Khvorova 368 Plantation Street, Albert Sherman Center Worcester, MA 01655, USA E-mail:
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19
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Chauhan P, Wadhwa K, Singh G. Caenorhabditis elegans as a model system to evaluate neuroprotective potential of nano formulations. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.1018754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The impact of neurodegenerative illnesses on society is significant, but the mechanisms leading to neuronal malfunction and death in these conditions remain largely unknown despite identifying essential disease genes. To pinpoint the mechanisms behind the pathophysiology of neurodegenerative diseases, several researchers have turned to nematode C. elegans instead of using mammals. Since C. elegans is transparent, free-living, and amenable to culture, it has several benefits. As a result, all the neurons in C. elegans can be easily identified, and their connections are understood. Human proteins linked to Neurodegeneration can be made to express in them. It is also possible to analyze how C. elegans orthologs of the genes responsible for human neurodegenerative diseases function. In this article, we focused at some of the most important C. elegans neurodegeneration models that accurately represent many elements of human neurodegenerative illness. It has been observed that studies using the adaptable C. elegans have helped us in better understanding of human diseases. These studies have used it to replicate several aspects of human neurodegeneration. A nanotech approach involves engineering materials or equipments interacting with biological systems at the molecular level to trigger physiological responses by increasing stimulation, responding, and interacting with target sites while minimizing side effects, thus revolutionizing the treatment and diagnosis of neurodegenerative diseases. Nanotechnologies are being used to treat neurological disorders and deliver nanoscale drugs. This review explores the current and future uses of these nanotechnologies as innovative therapeutic modalities in treatment of neurodegenerative diseases using C elegans as an experimental model.
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20
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Grice SJ, Liu JL. Motor defects in a Drosophila model for spinal muscular atrophy result from SMN depletion during early neurogenesis. PLoS Genet 2022; 18:e1010325. [PMID: 35877682 PMCID: PMC9352204 DOI: 10.1371/journal.pgen.1010325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/04/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Spinal muscular atrophy (SMA) is the most common autosomal recessive neurodegenerative disease, and is characterised by spinal motor neuron loss, impaired motor function and, often, premature death. Mutations and deletions in the widely expressed survival motor neuron 1 (SMN1) gene cause SMA; however, the mechanisms underlying the selectivity of motor neuron degeneration are not well understood. Although SMA is degenerative in nature, SMN function during embryonic and early postnatal development appears to be essential for motor neuron survival in animal models and humans. Notwithstanding, how developmental defects contribute to the subversion of postnatal and adult motor function remains elusive. Here, in a Drosophila SMA model, we show that neurodevelopmental defects precede gross locomotor dysfunction in larvae. Furthermore, to specifically address the relevance of SMN during neurogenesis and in neurogenic cell types, we show that SMN knockdown using neuroblast-specific and pan-neuronal drivers, but not differentiated neuron or glial cell drivers, impairs adult motor function. Using targeted knockdown, we further restricted SMN manipulation in neuroblasts to a defined time window. Our aim was to express specifically in the neuronal progenitor cell types that have not formed synapses, and thus a time that precedes neuromuscular junction formation and maturation. By restoring SMN levels in these distinct neuronal population, we partially rescue the larval locomotor defects of Smn mutants. Finally, combinatorial SMN knockdown in immature and mature neurons synergistically enhances the locomotor and survival phenotypes. Our in-vivo study is the first to directly rescue the motor defects of an SMA model by expressing Smn in an identifiable population of Drosophila neuroblasts and developing neurons, highlighting that neuronal sensitivity to SMN loss may arise before synapse establishment and nerve cell maturation. Spinal muscular atrophy (SMA) is the most common genetic cause of infant mortality and leads to the degeneration of the nerves that control muscle function. Loss-of-function mutations in the widely expressed survival motor neuron 1 (SMN1) gene cause SMA, but how low levels of SMN protein cause the neuronal dysfunction is not known. Although SMA is a disease of nerve degeneration, SMN function during nerve cell development may be important, particularly in severe forms of SMA. Nevertheless, how the defects during development and throughout early life contribute to the disease is not well understood. We have previously demonstrated that SMN protein becomes enriched in neuroblasts, which are the cells that divide to produce neurons. In the present study, motor defects observed in our fly model for SMA could be rescued by restoring SMN in neuroblasts alone. In addition, we show that knocking down SMN in healthy flies within the same cell type causes impaired motor function. The present study shows that the manipulation of SMN in a developmentally important cell type can cause motor defects, indicating that a period of abnormal neurodevelopment may contribute to SMA.
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Affiliation(s)
- Stuart J. Grice
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (SJG); , (J-LL)
| | - Ji-Long Liu
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- School of Life Science and Technology, Shanghai, Tech University, Shanghai, China
- * E-mail: (SJG); , (J-LL)
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21
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Ruffini N, Klingenberg S, Heese R, Schweiger S, Gerber S. The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. Front Aging Neurosci 2022; 14:866886. [PMID: 35832065 PMCID: PMC9271745 DOI: 10.3389/fnagi.2022.866886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022] Open
Abstract
The common features of all neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis (ALS), and Huntington's disease, are the accumulation of aggregated and misfolded proteins and the progressive loss of neurons, leading to cognitive decline and locomotive dysfunction. Still, they differ in their ultimate manifestation, the affected brain region, and the kind of proteinopathy. In the last decades, a vast number of processes have been described as associated with neurodegenerative diseases, making it increasingly harder to keep an overview of the big picture forming from all those data. In this meta-study, we analyzed genomic, transcriptomic, proteomic, and epigenomic data of the aforementioned diseases using the data of 234 studies in a network-based approach to study significant general coherences but also specific processes in individual diseases or omics levels. In the analysis part, we focus on only some of the emerging findings, but trust that the meta-study provided here will be a valuable resource for various other researchers focusing on specific processes or genes contributing to the development of neurodegeneration.
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Affiliation(s)
- Nicolas Ruffini
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Leibniz Institute for Resilience Research, Leibniz Association, Mainz, Germany
| | - Susanne Klingenberg
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Raoul Heese
- Fraunhofer Institute for Industrial Mathematics (ITWM), Kaiserslautern, Germany
| | - Susann Schweiger
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
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22
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circ-Pank1 promotes dopaminergic neuron neurodegeneration through modulating miR-7a-5p/α-syn pathway in Parkinson's disease. Cell Death Dis 2022; 13:477. [PMID: 35589691 PMCID: PMC9120029 DOI: 10.1038/s41419-022-04934-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 12/14/2022]
Abstract
Circular RNA (circRNA) is a type of non-coding RNA that is widely expressed in mammals. It is highly conserved and abundantly expressed in the brain. Here, we report the regulatory role of circRNA derived from the pantothenate kinase 1 (Pank1) gene (circ-Pank1) in Parkinson's disease (PD). Circ-Pank1 is highly expressed in the substantia nigra (SN) of PD model mice treated with rotenone and in the MN9D cell model of dopaminergic neurons. The circ-Pank1 knockdown ameliorated dopaminergic neuron damage and locomotor dysfunction after the treatment with rotenone. We found that circ-Pank1 could adsorb miR-7a-5p and upregulate the expression of α-synuclein (α-syn), which is a molecular hallmark closely related to PD. The inhibition of miR-7a-5p reversed the circ-Pank1 knockdown-induced amelioration of dopaminergic neuron injury. In conclusion, circ-Pank1 is overexpressed in PD and enhances the locomotor dysfunction via the miR-7a-5p/α-syn signaling axis. We revealed the functional role of circRNAs in the progression of PD and provided a potential target for noncoding RNAs in delaying the progression of PD.
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23
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Sproviero D, Gagliardi S, Zucca S, Arigoni M, Giannini M, Garofalo M, Fantini V, Pansarasa O, Avenali M, Ramusino MC, Diamanti L, Minafra B, Perini G, Zangaglia R, Costa A, Ceroni M, Calogero RA, Cereda C. Extracellular Vesicles Derived From Plasma of Patients With Neurodegenerative Disease Have Common Transcriptomic Profiling. Front Aging Neurosci 2022; 14:785741. [PMID: 35250537 PMCID: PMC8889100 DOI: 10.3389/fnagi.2022.785741] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/13/2022] [Indexed: 11/15/2022] Open
Abstract
Objectives There is a lack of effective biomarkers for neurodegenerative diseases (NDs) such as Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia. Extracellular vesicle (EV) RNA cargo can have an interesting potential as a non-invasive biomarker for NDs. However, the knowledge about the abundance of EV-mRNAs and their contribution to neurodegeneration is not clear. Methods Large and small EVs (LEVs and SEVs) were isolated from plasma of patients and healthy volunteers (control, CTR) by differential centrifugation and filtration, and RNA was extracted. Whole transcriptome was carried out using next generation sequencing (NGS). Results Coding RNA (i.e., mRNA) but not long non-coding RNAs (lncRNAs) in SEVs and LEVs of patients with ALS could be distinguished from healthy CTRs and from other NDs using the principal component analysis (PCA). Some mRNAs were found in commonly deregulated between SEVs of patients with ALS and frontotemporal dementia (FTD), and they were classified in mRNA processing and splicing pathways. In LEVs, instead, one mRNA and one antisense RNA (i.e., MAP3K7CL and AP003068.3) were found to be in common among ALS, FTD, and PD. No deregulated mRNAs were found in EVs of patients with AD. Conclusion Different RNA regulation occurs in LEVs and SEVs of NDs. mRNAs and lncRNAs are present in plasma-derived EVs of NDs, and there are common and specific transcripts that characterize LEVs and SEVs from the NDs considered in this study.
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Affiliation(s)
- Daisy Sproviero
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Stella Gagliardi
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
- *Correspondence: Stella Gagliardi
| | - Susanna Zucca
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
- EnGenome SRL, Pavia, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, Bioinformatics and Genomics Unit, University of Turin, Turin, Italy
| | - Marta Giannini
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Maria Garofalo
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
- Department of Biology and Biotechnology (“L. Spallanzani”), University of Pavia, Pavia, Italy
| | - Valentina Fantini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Laboratory of Neurobiology and Neurogenetic, Golgi-Cenci Foundation, Milan, Italy
| | - Orietta Pansarasa
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Micol Avenali
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Neurorehabilitation Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Matteo Cotta Ramusino
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Unit of Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Luca Diamanti
- Neuro-Oncology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (SRCCS) Mondino Foundation, Pavia, Italy
| | - Brigida Minafra
- Parkinson Disease and Movement Disorders Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Giulia Perini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Unit of Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Roberta Zangaglia
- Parkinson Disease and Movement Disorders Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Alfredo Costa
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Unit of Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Mauro Ceroni
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Unit of Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Raffaele A. Calogero
- Department of Molecular Biotechnology and Health Sciences, Bioinformatics and Genomics Unit, University of Turin, Turin, Italy
| | - Cristina Cereda
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
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Gilodi M, Lisi S, F. Dudás E, Fantini M, Puglisi R, Louka A, Marcatili P, Cattaneo A, Pastore A. Selection and Modelling of a New Single-Domain Intrabody Against TDP-43. Front Mol Biosci 2022; 8:773234. [PMID: 35237655 PMCID: PMC8884700 DOI: 10.3389/fmolb.2021.773234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder associated to deteriorating motor and cognitive functions, and short survival. The disease is caused by neuronal death which results in progressive muscle wasting and weakness, ultimately leading to lethal respiratory failure. The misbehaviour of a specific protein, TDP-43, which aggregates and becomes toxic in ALS patient’s neurons, is supposed to be one of the causes. TDP-43 is a DNA/RNA-binding protein involved in several functions related to nucleic acid metabolism. Sequestration of TDP-43 aggregates is a possible therapeutic strategy that could alleviate or block pathology. Here, we describe the selection and characterization of a new intracellular antibody (intrabody) against TDP-43 from a llama nanobody library. The structure of the selected intrabody was predicted in silico and the model was used to suggest mutations that enabled to improve its expression yield, facilitating its experimental validation. We showed how coupling experimental methodologies with in silico design may allow us to obtain an antibody able to recognize the RNA binding regions of TDP-43. Our findings illustrate a strategy for the mitigation of TDP-43 proteinopathy in ALS and provide a potential new tool for diagnostics.
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Affiliation(s)
- Martina Gilodi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Simonetta Lisi
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Erika F. Dudás
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Marco Fantini
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Rita Puglisi
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Alexandra Louka
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Paolo Marcatili
- Department of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
- *Correspondence: Annalisa Pastore, ; Antonino Cattaneo,
| | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- *Correspondence: Annalisa Pastore, ; Antonino Cattaneo,
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25
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Ebrahimi V, Tarhriz V, Talebi M, Rasouli A, Farjami A, Razi Soofiyani S, Soleimanian A, Forouhandeh H. A new insight on feasibility of pre-, pro-, and synbiotics-based therapies in Alzheimer’s disease. JOURNAL OF REPORTS IN PHARMACEUTICAL SCIENCES 2022. [DOI: 10.4103/jrptps.jrptps_170_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Ruffo P, Strafella C, Cascella R, Caputo V, Conforti FL, Andò S, Giardina E. Deregulation of ncRNA in Neurodegenerative Disease: Focus on circRNA, lncRNA and miRNA in Amyotrophic Lateral Sclerosis. Front Genet 2021; 12:784996. [PMID: 34925464 PMCID: PMC8674781 DOI: 10.3389/fgene.2021.784996] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 01/17/2023] Open
Abstract
Parallel and massive sequencing of total RNA samples derived from different samples are possible thanks to the use of NGS (Next Generation Sequencing) technologies. This allowed characterizing the transcriptomic profile of both cell and tissue populations, increasing the knowledge of the molecular pathological processes of complex diseases, such as neurodegenerative diseases (NDs). Among the NDs, Amyotrophic Lateral Sclerosis (ALS) is caused by the progressive loss of motor neurons (MNs), and, to date, the diagnosis is often made by exclusion because there is no specific symptomatologic picture. For this reason, it is important to search for biomarkers that are clinically useful for carrying out a fast and accurate diagnosis of ALS. Thanks to various studies, it has been possible to propose several molecular mechanisms associated with the disease, some of which include the action of non-coding RNA, including circRNAs, miRNAs, and lncRNAs which will be discussed in the present review. The evidence analyzed in this review highlights the importance of conducting studies to better characterize the different ncRNAs in the disease to use them as possible diagnostic, prognostic, and/or predictive biomarkers of ALS and other NDs.
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Affiliation(s)
- Paola Ruffo
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Sebastiano Andò
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
- Centro Sanitario, University of Calabria, Arcavacata di Rende, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
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27
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RNA Modifications and RNA Metabolism in Neurological Disease Pathogenesis. Int J Mol Sci 2021; 22:ijms222111870. [PMID: 34769301 PMCID: PMC8584444 DOI: 10.3390/ijms222111870] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/16/2021] [Accepted: 10/26/2021] [Indexed: 02/06/2023] Open
Abstract
The intrinsic cellular heterogeneity and molecular complexity of the mammalian nervous system relies substantially on the dynamic nature and spatiotemporal patterning of gene expression. These features of gene expression are achieved in part through mechanisms involving various epigenetic processes such as DNA methylation, post-translational histone modifications, and non-coding RNA activity, amongst others. In concert, another regulatory layer by which RNA bases and sugar residues are chemically modified enhances neuronal transcriptome complexity. Similar RNA modifications in other systems collectively constitute the cellular epitranscriptome that integrates and impacts various physiological processes. The epitranscriptome is dynamic and is reshaped constantly to regulate vital processes such as development, differentiation and stress responses. Perturbations of the epitranscriptome can lead to various pathogenic conditions, including cancer, cardiovascular abnormalities and neurological diseases. Recent advances in next-generation sequencing technologies have enabled us to identify and locate modified bases/sugars on different RNA species. These RNA modifications modulate the stability, transport and, most importantly, translation of RNA. In this review, we discuss the formation and functions of some frequently observed RNA modifications—including methylations of adenine and cytosine bases, and isomerization of uridine to pseudouridine—at various layers of RNA metabolism, together with their contributions to abnormal physiological conditions that can lead to various neurodevelopmental and neurological disorders.
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28
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Sekulovski S, Devant P, Panizza S, Gogakos T, Pitiriciu A, Heitmeier K, Ramsay EP, Barth M, Schmidt C, Tuschl T, Baas F, Weitzer S, Martinez J, Trowitzsch S. Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia. Nat Commun 2021; 12:5610. [PMID: 34584079 PMCID: PMC8479045 DOI: 10.1038/s41467-021-25870-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Introns of human transfer RNA precursors (pre-tRNAs) are excised by the tRNA splicing endonuclease TSEN in complex with the RNA kinase CLP1. Mutations in TSEN/CLP1 occur in patients with pontocerebellar hypoplasia (PCH), however, their role in the disease is unclear. Here, we show that intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers independently of CLP1. Splice site recognition involves the mature domain and the anticodon-intron base pair of pre-tRNAs. The 2.1-Å resolution X-ray crystal structure of a TSEN15–34 heterodimer and differential scanning fluorimetry analyses show that PCH mutations cause thermal destabilization. While endonuclease activity in recombinant mutant TSEN is unaltered, we observe assembly defects and reduced pre-tRNA cleavage activity resulting in an imbalanced pre-tRNA pool in PCH patient-derived fibroblasts. Our work defines the molecular principles of intron excision in humans and provides evidence that modulation of TSEN stability may contribute to PCH phenotypes. Mutations within subunits of the tRNA splicing endonuclease complex (TSEN) are associated with pontocerebellar hypoplasia (PCH). Here the authors show that tRNA intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers, and provide evidence that modulation of TSEN stability may contribute to PCH phenotypes.
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Affiliation(s)
- Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Pascal Devant
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany.,Ph.D. Program in Virology, Harvard Medical School, Boston, MA, USA.,Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Silvia Panizza
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Tasos Gogakos
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Anda Pitiriciu
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Katharina Heitmeier
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | | | - Marie Barth
- Interdisciplinary research center HALOmem, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary research center HALOmem, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Thomas Tuschl
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Frank Baas
- Department of Clinical Genetics, Leiden University, Leiden, Netherlands
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany.
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29
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Rey F, Marcuzzo S, Bonanno S, Bordoni M, Giallongo T, Malacarne C, Cereda C, Zuccotti GV, Carelli S. LncRNAs Associated with Neuronal Development and Oncogenesis Are Deregulated in SOD1-G93A Murine Model of Amyotrophic Lateral Sclerosis. Biomedicines 2021; 9:biomedicines9070809. [PMID: 34356873 PMCID: PMC8301400 DOI: 10.3390/biomedicines9070809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/04/2021] [Accepted: 07/08/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease caused in 10% of cases by inherited mutations considered “familial”. An ever-increasing amount of evidence is showing a fundamental role for RNA metabolism in ALS pathogenesis, and long non-coding RNAs (lncRNAs) appear to play a role in ALS development. Here, we aim to investigate the expression of a panel of lncRNAs (linc-Enc1, linc–Brn1a, linc–Brn1b, linc-p21, Hottip, Tug1, Eldrr, and Fendrr) which could be implicated in early phases of ALS. Via Real-Time PCR, we assessed their expression in a murine familial model of ALS (SOD1-G93A mouse) in brain and spinal cord areas of SOD1-G93A mice in comparison with that of B6.SJL control mice, in asymptomatic (week 8) and late-stage disease (week 18). We highlighted a specific area and pathogenetic-stage deregulation in each lncRNA, with linc-p21 being deregulated in all analyzed tissues. Moreover, we analyzed the expression of their human homologues in SH-SY5Y-SOD1-WT and SH-SY5Y-SOD1-G93A, observing a profound alteration in their expression. Interestingly, the lncRNAs expression in our ALS models often resulted opposite to that observed for the lncRNAs in cancer. These evidences suggest that lncRNAs could be novel disease-modifying agents, biomarkers, or pathways affected by ALS neurodegeneration.
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Affiliation(s)
- Federica Rey
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Via Grassi 74, 20157 Milano, Italy; (F.R.); (T.G.); (G.V.Z.)
- Paediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milano, 20157 Milano, Italy
| | - Stefania Marcuzzo
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133 Milan, Italy; (S.M.); (S.B.); (C.M.)
| | - Silvia Bonanno
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133 Milan, Italy; (S.M.); (S.B.); (C.M.)
| | - Matteo Bordoni
- Centro di Eccellenza Sulle Malattie Neurodegenerative, Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Università Degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy;
| | - Toniella Giallongo
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Via Grassi 74, 20157 Milano, Italy; (F.R.); (T.G.); (G.V.Z.)
- Paediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milano, 20157 Milano, Italy
| | - Claudia Malacarne
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133 Milan, Italy; (S.M.); (S.B.); (C.M.)
- PhD Program in Neuroscience, University of Milano-Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, 27100 Pavia, Italy;
| | - Gian Vincenzo Zuccotti
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Via Grassi 74, 20157 Milano, Italy; (F.R.); (T.G.); (G.V.Z.)
- Paediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milano, 20157 Milano, Italy
- Department of Pediatrics, Children’s Hospital “V. Buzzi”, Via Lodovico Castelvetro 32, 20154 Milano, Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Via Grassi 74, 20157 Milano, Italy; (F.R.); (T.G.); (G.V.Z.)
- Paediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milano, 20157 Milano, Italy
- Correspondence: ; Tel.: +39-02-50319825
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30
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Shi WZ, Li W, Cheng Y, Zhang M, Niu XC, Gao QW, Lu Y, Tian T, Du S, Mi Y, Chang MZ, Tian Y. The cytoprotective role of omentin against oxidative stress-induced PC12 apoptosis. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2021; 49:483-492. [PMID: 34151664 DOI: 10.1080/21691401.2021.1892707] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Oxidative stress has been proven to play a critical role in the pathogenesis of neuronal injury. As a novel adipocytokine, omentin is produced by visceral adipose with insulin sensitizing effects and has been revealed to possess anti-inflammatory effects. However, the possible effect of omentin on oxidative stress remains unknown. The present study aimed to detect the potential protective effect of omentin against hydrogen peroxide (H2O2)-induced cytotoxicity of PC12 cells. The results showed that no cytotoxic effect was shown in PC12 cells co-cultured with omentin alone at a concentration of 50-1000 ng/mL. The CCK8 and TUNEL assays suggested that omentin could remarkably attenuate apoptosis induced by 100 μM H2O2. The PCR and western blotting showed that the expression levels of Bax was significantly inhibited by omentin via the upregulation of miR-128-3p at its 3'-UTR. Taken together, these results indicated that omentin protects PC12 cells against H2O2-induced apoptosis, and further studies need to be conducted before utilization in the clinic for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Wen-Zhen Shi
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China.,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Wu Li
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Ye Cheng
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Meng Zhang
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Xiao-Chen Niu
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Qi-Wei Gao
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
| | - Ying Lu
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China.,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China.,Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Tian Tian
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China.,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China.,Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Shan Du
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China.,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China.,Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Yan Mi
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China.,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China.,Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Ming-Ze Chang
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China.,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Ye Tian
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China.,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China.,Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
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31
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Onaolapo OJ, Onaolapo AY, Olowe OA, Udoh MO, Udoh DO, Nathaniel TI. Melatonin and Melatonergic Influence on Neuronal Transcription Factors: Implications for the Development of Novel Therapies for Neurodegenerative Disorders. Curr Neuropharmacol 2021; 18:563-577. [PMID: 31885352 PMCID: PMC7457420 DOI: 10.2174/1570159x18666191230114339] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/16/2019] [Accepted: 12/28/2019] [Indexed: 01/04/2023] Open
Abstract
Melatonin is a multifunctional signalling molecule that is secreted by the mammalian pineal gland, and also found in a number of organisms including plants and bacteria. Research has continued to uncover an ever-increasing number of processes in which melatonin is known to play crucial roles in mammals. Amongst these functions is its contribution to cell multiplication, differentiation and survival in the brain. Experimental studies show that melatonin can achieve these functions by influencing transcription factors which control neuronal and glial gene expression. Since neuronal survival and differentiation are processes that are important determinants of the pathogenesis, course and outcome of neurodegenerative disorders; the known and potential influences of melatonin on neuronal and glial transcription factors are worthy of constant examination. In this review, relevant scientific literature on the role of melatonin in preventing or altering the course and outcome of neurodegenerative disorders, by focusing on melatonin's influence on transcription factors is examined. A number of transcription factors whose functions can be influenced by melatonin in neurodegenerative disease models have also been highlighted. Finally, the therapeutic implications of melatonin's influences have also been discussed and the potential limitations to its applications have been highlighted.
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Affiliation(s)
- Olakunle J. Onaolapo
- Behavioural Neuroscience/Neuropharmacology Unit, Department of Pharmacology, Ladoke Akintola University of Technology, Osogbo, Osun State, Nigeria
| | - Adejoke Y. Onaolapo
- Behavioural Neuroscience/Neurobiology Unit, Department of Anatomy, Ladoke Akintola University of Technology, Ogbomosho, Oyo State, Nigeria
| | - Olugbenga A. Olowe
- Molecular Bacteriology and Immunology Unit, Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Osogbo, Osun State, Nigeria
| | - Mojisola O. Udoh
- Department of Pathology, University of Benin Teaching Hospital, Benin City, Nigeria
| | - David O. Udoh
- Division of Neurological Surgery, Department of Surgery, University of Benin Teaching Hospital, Benin City, Edo State, Nigeria
| | - Thomas I. Nathaniel
- University of South Carolina School of Medicine-Greenville, Greenville, South Carolina, 29605, United States
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Ishiguro T, Nagai Y, Ishikawa K. Insight Into Spinocerebellar Ataxia Type 31 (SCA31) From Drosophila Model. Front Neurosci 2021; 15:648133. [PMID: 34113230 PMCID: PMC8185138 DOI: 10.3389/fnins.2021.648133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/31/2021] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia type 31 (SCA31) is a progressive neurodegenerative disease characterized by degeneration of Purkinje cells in the cerebellum. Its genetic cause is a 2.5- to 3.8-kb-long complex pentanucleotide repeat insertion containing (TGGAA)n, (TAGAA)n, (TAAAA)n, and (TAAAATAGAA)n located in an intron shared by two different genes: brain expressed associated with NEDD4-1 (BEAN1) and thymidine kinase 2 (TK2). Among these repeat sequences, (TGGAA)n repeat was the only sequence segregating with SCA31, which strongly suggests its pathogenicity. In SCA31 patient brains, the mutant BEAN1 transcript containing expanded UGGAA repeats (UGGAAexp) was found to form abnormal RNA structures called RNA foci in cerebellar Purkinje cell nuclei. In addition, the deposition of pentapeptide repeat (PPR) proteins, poly(Trp-Asn-Gly-Met-Glu), translated from UGGAAexp RNA, was detected in the cytoplasm of Purkinje cells. To uncover the pathogenesis of UGGAAexp in SCA31, we generated Drosophila models of SCA31 expressing UGGAAexp RNA. The toxicity of UGGAAexp depended on its length and expression level, which was accompanied by the accumulation of RNA foci and translation of repeat-associated PPR proteins in Drosophila, consistent with the observation in SCA31 patient brains. We also revealed that TDP-43, FUS, and hnRNPA2B1, motor neuron disease–linked RNA-binding proteins bound to UGGAAexp RNA, act as RNA chaperones to regulate the formation of RNA foci and repeat-associated translation. Further research on the role of RNA-binding proteins as RNA chaperones may also provide a novel therapeutic strategy for other microsatellite repeat expansion diseases besides SCA31.
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Affiliation(s)
- Taro Ishiguro
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University, Bunkyo City, Japan
| | - Yoshitaka Nagai
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kinya Ishikawa
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University, Bunkyo City, Japan.,Department of Personalized Genomic Medicine for Health, Graduate School, Tokyo Medical and Dental University, Bunkyo City, Japan
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33
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Kelaini S, Chan C, Cornelius VA, Margariti A. RNA-Binding Proteins Hold Key Roles in Function, Dysfunction, and Disease. BIOLOGY 2021; 10:biology10050366. [PMID: 33923168 PMCID: PMC8146904 DOI: 10.3390/biology10050366] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
RNA-binding proteins (RBPs) are multi-faceted proteins in the regulation of RNA or its RNA splicing, localisation, stability, and translation. Amassing proof from many recent and dedicated studies reinforces the perception of RBPs exerting control through differing expression levels, cellular localization and post-transcriptional alterations. However, since the regulation of RBPs is reliant on the micro-environment and events like stress response and metabolism, their binding affinities and the resulting RNA-RBP networks may be affected. Therefore, any misregulation and disruption in the features of RNA and its related homeostasis can lead to a number of diseases that include diabetes, cardiovascular disease, and other disorders such as cancer and neurodegenerative diseases. As such, correct regulation of RNA and RBPs is crucial to good health as the effect RBPs exert through loss of function can cause pathogenesis. In this review, we will discuss the significance of RBPs and their typical function and how this can be disrupted in disease.
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Clarke JP, Thibault PA, Salapa HE, Levin MC. A Comprehensive Analysis of the Role of hnRNP A1 Function and Dysfunction in the Pathogenesis of Neurodegenerative Disease. Front Mol Biosci 2021; 8:659610. [PMID: 33912591 PMCID: PMC8072284 DOI: 10.3389/fmolb.2021.659610] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a member of the hnRNP family of conserved proteins that is involved in RNA transcription, pre-mRNA splicing, mRNA transport, protein translation, microRNA processing, telomere maintenance and the regulation of transcription factor activity. HnRNP A1 is ubiquitously, yet differentially, expressed in many cell types, and due to post-translational modifications, can vary in its molecular function. While a plethora of knowledge is known about the function and dysfunction of hnRNP A1 in diseases other than neurodegenerative disease (e.g., cancer), numerous studies in amyotrophic lateral sclerosis, frontotemporal lobar degeneration, multiple sclerosis, spinal muscular atrophy, Alzheimer’s disease, and Huntington’s disease have found that the dysregulation of hnRNP A1 may contribute to disease pathogenesis. How hnRNP A1 mechanistically contributes to these diseases, and whether mutations and/or altered post-translational modifications contribute to pathogenesis, however, is currently under investigation. The aim of this comprehensive review is to first describe the background of hnRNP A1, including its structure, biological functions in RNA metabolism and the post-translational modifications known to modify its function. With this knowledge, the review then describes the influence of hnRNP A1 in neurodegenerative disease, and how its dysfunction may contribute the pathogenesis.
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Affiliation(s)
- Joseph P Clarke
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada
| | - Patricia A Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada.,Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hannah E Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada.,Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Michael C Levin
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada.,Division of Neurology, Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
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35
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Amado DA, Davidson BL. Gene therapy for ALS: A review. Mol Ther 2021; 29:3345-3358. [PMID: 33839324 DOI: 10.1016/j.ymthe.2021.04.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/28/2021] [Accepted: 04/05/2021] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) has historically posed unique challenges for gene-therapy-based approaches, due to a paucity of therapeutic targets as well as the difficulty of accessing both the brain and spinal cord. Recent advances in our understanding of disease mechanism and ALS genetics, however, have combined with tremendous strides in CNS targeting, gene delivery, and gene editing and knockdown techniques to open new horizons of therapeutic possibility. Gene therapy clinical trials are currently underway for ALS patients with SOD1 mutations, C9orf72 hexanucleotide repeat expansions, ATXN2 trinucleotide expansions, and FUS mutations, as well as sporadic disease without known genetic cause. In this review, we provide an in-depth exploration of the state of ALS-directed gene therapy, including antisense oligonucleotides, RNA interference, CRISPR, adeno-associated virus (AAV)-mediated trophic support, and antibody-based methods. We discuss how each of these approaches has been implemented across known genetic causes as well as sporadic ALS, reviewing preclinical studies as well as completed and ongoing human clinical trials. We highlight the transformative potential of these evolving technologies as the gene therapy field advances toward a true disease-modifying treatment for this devastating illness.
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Affiliation(s)
- Defne A Amado
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Beverly L Davidson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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36
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McMahon M, Forester C, Buffenstein R. Aging through an epitranscriptomic lens. NATURE AGING 2021; 1:335-346. [PMID: 37117595 DOI: 10.1038/s43587-021-00058-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/08/2021] [Indexed: 04/30/2023]
Abstract
The mechanistic causes of aging, the time-related decline in function and good health that leads to increased mortality, remain poorly understood. Here we propose that age-dependent alteration of the epitranscriptome, encompassing more than 150 chemically distinct post-transcriptional modifications or editing events, warrants exploration as an important modulator of aging. The epitranscriptome is a potent regulator of RNA function, diverse cellular processes and tissue regenerative capacity. To date, only a few studies link alterations in the epitranscriptome to molecular and physiological changes during aging; however, epitranscriptome dysfunction is associated with and underlies several age-associated pathologies, including cancer and neurodegenerative, cardiovascular and autoimmune diseases. For example, changes in RNA modifications (such as N6-methyladenosine and inosine) impact cardiac physiology and are linked to cardiac fibrosis. Although an uncharted research focus, mapping epitranscriptome alterations in the context of aging may elucidate novel predictors of both health and lifespan, and may identify therapeutic targets for attenuating aging and abrogating age-related diseases.
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Affiliation(s)
- Mary McMahon
- Calico Life Sciences LLC, South San Francisco, CA, USA.
| | - Craig Forester
- Department of Pediatrics, University of Colorado, Denver, CO, USA
- Children's Hospital Colorado, Division of Pediatric Hematology/Oncology/Bone Marrow Transplant, Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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37
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Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22073296. [PMID: 33804860 PMCID: PMC8036390 DOI: 10.3390/ijms22073296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 12/12/2022] Open
Abstract
The transcriptional regulator peroxisome proliferator activated receptor gamma coactivator 1A (PGC-1α), encoded by PPARGC1A, has been linked to neurodegenerative diseases. Recently discovered CNS-specific PPARGC1A transcripts are initiated far upstream of the reference promoter, spliced to exon 2 of the reference gene, and are more abundant than reference gene transcripts in post-mortem human brain samples. The proteins translated from the CNS and reference transcripts differ only at their N-terminal regions. To dissect functional differences between CNS-specific isoforms and reference proteins, we used clustered regularly interspaced short palindromic repeats transcriptional activation (CRISPRa) for selective endogenous activation of the CNS or the reference promoters in SH-SY5Y cells. Expression and/or exon usage of the targets was ascertained by RNA sequencing. Compared to controls, more differentially expressed genes were observed after activation of the CNS than the reference gene promoter, while the magnitude of alternative exon usage was comparable between activation of the two promoters. Promoter-selective associations were observed with canonical signaling pathways, mitochondrial and nervous system functions and neurological diseases. The distinct N-terminal as well as the shared downstream regions of PGC-1α isoforms affect the exon usage of numerous genes. Furthermore, associations of risk genes of amyotrophic lateral sclerosis and Parkinson's disease were noted with differentially expressed genes resulting from the activation of the CNS and reference gene promoter, respectively. Thus, CNS-specific isoforms markedly amplify the biological functions of PPARGC1A and CNS-specific isoforms and reference proteins have common, complementary and selective functions relevant for neurodegenerative diseases.
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38
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Guo Q, Dammer EB, Zhou M, Kundinger SR, Gearing M, Lah JJ, Levey AI, Shulman JM, Seyfried NT. Targeted Quantification of Detergent-Insoluble RNA-Binding Proteins in Human Brain Reveals Stage and Disease Specific Co-aggregation in Alzheimer's Disease. Front Mol Neurosci 2021; 14:623659. [PMID: 33815056 PMCID: PMC8014091 DOI: 10.3389/fnmol.2021.623659] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/12/2021] [Indexed: 01/02/2023] Open
Abstract
Core spliceosome and related RNA-binding proteins aggregate in Alzheimer’s disease (AD) brain even in early asymptomatic stages (AsymAD) of disease. To assess the specificity of RNA-binding protein aggregation in AD, we developed a targeted mass spectrometry approach to quantify broad classes of RNA-binding proteins with other pathological proteins including tau and amyloid beta (Aβ) in detergent insoluble fractions from control, AsymAD, AD and Parkinson’s disease (PD) brain. Relative levels of specific insoluble RNA-binding proteins across different disease groups correlated with accumulation of Aβ and tau aggregates. RNA-binding proteins, including splicing factors with homology to the basic-acidic dipeptide repeats of U1-70K, preferentially aggregated in AsymAD and AD. In contrast, PD brain aggregates were relatively depleted of many RNA-binding proteins compared to AsymAD and AD groups. Correlation network analyses resolved 29 distinct modules of co-aggregating proteins including modules linked to spliceosome assembly, nuclear speckles and RNA splicing. Modules related to spliceosome assembly and nuclear speckles showed stage-specific enrichment of insoluble RBPs from AsymAD and AD brains, whereas the RNA splicing module was reduced specifically in PD. Collectively, this work identifies classes of RNA-binding proteins that distinctly co-aggregate in detergent-insoluble fractions across the specific neurodegenerative diseases we examined.
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Affiliation(s)
- Qi Guo
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States
| | - Eric B Dammer
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States.,Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States
| | - Maotian Zhou
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States
| | - Sean R Kundinger
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States
| | - Marla Gearing
- Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Neurology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Neurology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Joshua M Shulman
- Departments of Neurology, Neuroscience and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | - Nicholas T Seyfried
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States.,Goizueta Alzheimer's Disease Research Center, School of Medicine, Emory University, Atlanta, GA, United States.,Department of Neurology, School of Medicine, Emory University, Atlanta, GA, United States
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39
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Sproviero D, Gagliardi S, Zucca S, Arigoni M, Giannini M, Garofalo M, Olivero M, Dell’Orco M, Pansarasa O, Bernuzzi S, Avenali M, Cotta Ramusino M, Diamanti L, Minafra B, Perini G, Zangaglia R, Costa A, Ceroni M, Perrone-Bizzozero NI, Calogero RA, Cereda C. Different miRNA Profiles in Plasma Derived Small and Large Extracellular Vesicles from Patients with Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22052737. [PMID: 33800495 PMCID: PMC7962970 DOI: 10.3390/ijms22052737] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Identifying biomarkers is essential for early diagnosis of neurodegenerative diseases (NDs). Large (LEVs) and small extracellular vesicles (SEVs) are extracellular vesicles (EVs) of different sizes and biological functions transported in blood and they may be valid biomarkers for NDs. The aim of our study was to investigate common and different miRNA signatures in plasma derived LEVs and SEVs of Alzheimer’s disease (AD), Parkinson’s disease (PD), Amyotrophic Lateral Sclerosis (ALS) and Fronto-Temporal Dementia (FTD) patients. LEVs and SEVs were isolated from plasma of patients and healthy volunteers (CTR) by filtration and differential centrifugation and RNA was extracted. Small RNAs libraries were carried out by Next Generation Sequencing (NGS). MiRNAs discriminate all NDs diseases from CTRs and they can provide a signature for each NDs. Common enriched pathways for SEVs were instead linked to ubiquitin mediated proteolysis and Toll-like receptor signaling pathways and for LEVs to neurotrophin signaling and Glycosphingolipid biosynthesis pathway. LEVs and SEVs are involved in different pathways and this might give a specificity to their role in the spreading of the disease. The study of common and different miRNAs transported by LEVs and SEVs can be of great interest for biomarker discovery and for pathogenesis studies in neurodegeneration.
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Affiliation(s)
- Daisy Sproviero
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (D.S.); (S.G.); (S.Z.); (M.G.); (M.G.); (O.P.)
| | - Stella Gagliardi
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (D.S.); (S.G.); (S.Z.); (M.G.); (M.G.); (O.P.)
| | - Susanna Zucca
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (D.S.); (S.G.); (S.Z.); (M.G.); (M.G.); (O.P.)
- EnGenome SRL, 27100 Pavia, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, Bioinformatics and Genomics Unit, University of Turin, 10126 Turin, Italy; (M.A.); (R.A.C.)
| | - Marta Giannini
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (D.S.); (S.G.); (S.Z.); (M.G.); (M.G.); (O.P.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Maria Garofalo
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (D.S.); (S.G.); (S.Z.); (M.G.); (M.G.); (O.P.)
- Department of Biology and Biotechnology (“L. Spallanzani”), University of Pavia, 27100 Pavia, Italy
| | - Martina Olivero
- Department of Oncology, University of Turin, 10060 Turin, Italy;
| | - Michela Dell’Orco
- Departments of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA;
| | - Orietta Pansarasa
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (D.S.); (S.G.); (S.Z.); (M.G.); (M.G.); (O.P.)
| | - Stefano Bernuzzi
- Immunohematological and Transfusional Service and Centre of Transplantation Immunology, IRCCS “San Matteo Foundation”, 27100 Pavia, Italy;
| | - Micol Avenali
- Neurorehabilitation Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy;
| | - Matteo Cotta Ramusino
- Unit of Behavioral Neurology, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.C.R.); (G.P.); (M.C.)
| | - Luca Diamanti
- Neuro-Oncology Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy;
| | - Brigida Minafra
- Parkinson Unit and Movement Disorders Mondino Foundation IRCCS, 27100 Pavia, Italy; (B.M.); (R.Z.)
| | - Giulia Perini
- Unit of Behavioral Neurology, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.C.R.); (G.P.); (M.C.)
| | - Roberta Zangaglia
- Parkinson Unit and Movement Disorders Mondino Foundation IRCCS, 27100 Pavia, Italy; (B.M.); (R.Z.)
| | - Alfredo Costa
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
- Unit of Behavioral Neurology, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.C.R.); (G.P.); (M.C.)
| | - Mauro Ceroni
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
- Unit of Behavioral Neurology, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.C.R.); (G.P.); (M.C.)
| | - Nora I. Perrone-Bizzozero
- Departments of Neurosciences and Psychiatry and Behavioral Health, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA;
| | - Raffaele A. Calogero
- Department of Molecular Biotechnology and Health Sciences, Bioinformatics and Genomics Unit, University of Turin, 10126 Turin, Italy; (M.A.); (R.A.C.)
| | - Cristina Cereda
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (D.S.); (S.G.); (S.Z.); (M.G.); (M.G.); (O.P.)
- Correspondence: ; Tel.: +39-0382380348
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40
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 368] [Impact Index Per Article: 122.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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Beutgen VM, Pfeiffer N, Grus FH. Serological Levels of Anti-clathrin Antibodies Are Decreased in Patients With Pseudoexfoliation Glaucoma. Front Immunol 2021; 12:616421. [PMID: 33679756 PMCID: PMC7933590 DOI: 10.3389/fimmu.2021.616421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Evidence for immunologic contribution to glaucoma pathophysiology is steadily increasing in ophthalmic research. Particularly, an altered abundance of circulating autoantibodies to ocular antigens is frequently observed. Here, we report an analysis of autoantibody abundancies to selected antigens in sera of open-angle glaucoma patients, subdivided into normal-tension glaucoma (N = 31), primary open-angle glaucoma (N = 43) and pseudoexfoliation glaucoma (N = 45), vs. a non-glaucomatous control group (N = 46). Serum samples were analyzed by protein microarray, including 38 antigens. Differences in antibody levels were assessed by ANOVA. Five serological antibodies showed significantly altered levels among the four groups (P < 0.05), which can be used to cluster the subjects in groups consisting mainly of PEXG or POAG/NTG samples. Among the altered autoantibodies, anti-Clathrin antibodies were identified as most important subgroup predictors, enhancing prospective glaucoma subtype prediction. As a second aim, we wanted to gain further insights into the characteristics of previously identified glaucoma-related antigens and their role in glaucoma pathogenesis. To this end, we used the bioinformatics toolset of Metascape to construct protein-protein interaction networks and GO enrichment analysis. Glaucoma-related antigens were significantly enriched in 13 biological processes, including mRNA metabolism, protein folding, blood coagulation and apoptosis, proposing a link of glaucoma-associated pathways to changes in the autoantibody repertoire. In conclusion, our study provides new aspects of the involvement of natural autoimmunity in glaucoma pathomechanisms and promotes advanced opportunities toward new diagnostic approaches.
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Affiliation(s)
- Vanessa M Beutgen
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Norbert Pfeiffer
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Franz H Grus
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
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tRNA Biology in the Pathogenesis of Diabetes: Role of Genetic and Environmental Factors. Int J Mol Sci 2021; 22:ijms22020496. [PMID: 33419045 PMCID: PMC7825315 DOI: 10.3390/ijms22020496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 02/07/2023] Open
Abstract
The global rise in type 2 diabetes results from a combination of genetic predisposition with environmental assaults that negatively affect insulin action in peripheral tissues and impair pancreatic β-cell function and survival. Nongenetic heritability of metabolic traits may be an important contributor to the diabetes epidemic. Transfer RNAs (tRNAs) are noncoding RNA molecules that play a crucial role in protein synthesis. tRNAs also have noncanonical functions through which they control a variety of biological processes. Genetic and environmental effects on tRNAs have emerged as novel contributors to the pathogenesis of diabetes. Indeed, altered tRNA aminoacylation, modification, and fragmentation are associated with β-cell failure, obesity, and insulin resistance. Moreover, diet-induced tRNA fragments have been linked with intergenerational inheritance of metabolic traits. Here, we provide a comprehensive review of how perturbations in tRNA biology play a role in the pathogenesis of monogenic and type 2 diabetes.
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Wong CE, Jin LW, Chu YP, Wei WY, Ho PC, Tsai KJ. TDP-43 proteinopathy impairs mRNP granule mediated postsynaptic translation and mRNA metabolism. Theranostics 2021; 11:330-345. [PMID: 33391478 PMCID: PMC7681104 DOI: 10.7150/thno.51004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Local protein synthesis and mRNA metabolism mediated by mRNP granules in the dendrites and the postsynaptic compartment is essential for synaptic remodeling and plasticity in neuronal cells. Dysregulation of these processes caused by TDP-43 proteinopathy leads to neurodegenerative diseases, such as frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Methods: Using biochemical analysis and imaging techniques, including super-resolution microscopy, we provide evidence, for the first time, for the postsynaptic localization of TDP-43 in mammalian synapses and we show that TDP-43 is a component of neuronal mRNP granules. Results: With activity stimulation and various molecular approaches, we further demonstrate activity-dependent mRNP granule dynamics involving disassembly of mRNP granules, release of mRNAs, activation of local protein translation, and the impairment of granule disassembly in cellular, animal and human models of TDP-43 proteinopathy. Conclusion: Our study elucidates the interplay between TDP-43 and neuronal mRNP granules in normal physiology and TDP-43 proteinopathy in the regulation of local protein translation and mRNA metabolism in the postsynaptic compartment.
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Affiliation(s)
- Chia-En Wong
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Lee-Way Jin
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, California, USA
| | - Yuan-Ping Chu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Yen Wei
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Chuan Ho
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Grinkevich LN. The role of microRNAs in learning and long-term memory. Vavilovskii Zhurnal Genet Selektsii 2020; 24:885-896. [PMID: 35088002 PMCID: PMC8763713 DOI: 10.18699/vj20.687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/11/2020] [Accepted: 10/15/2020] [Indexed: 01/10/2023] Open
Abstract
The mechanisms of long-term memory formation and ways to improve it (in the case of its impairment) remain an extremely difficult problem yet to be solved. Over the recent years, much attention has been
paid to microRNAs in this regard. MicroRNAs are unique endogenous non-coding RNAs about 22 nucleotides in
length; each can regulate translation of hundreds of messenger RNA targets, thereby controlling entire gene networks. MicroRNAs are widely represented in the central nervous system. A large number of studies are currently
being conducted to investigate the role of microRNAs in the brain functioning. A number of microRNAs have
been shown to be involved in the process of synaptic plasticity, as well as in the long-term memory formation.
Disruption of microRNA biogenesis leads to significant cognitive dysfunctions. Moreover, impaired microRNA
biogenesis is one of the causes of the pathogenesis of mental disorders, neurodegenerative illnesses and senile
dementia, which are often accompanied by deterioration in the learning ability and by memory impairment.
Optimistic predictions are made that microRNAs can be used as targets for therapeutic treatment and for diagnosing the above pathologies. The importance of applications related to microRNAs significantly raises interest
in studying their functions in the brain. Thus, this review is focused on the role of microRNAs in cognitive processes. It describes microRNA biogenesis and the role of miRNAs in the regulation of gene expression, as well
as the latest achievements in studying the functional role of microRNAs in learning and in long-term memory
formation, depending on the activation or inhibition of their expression. The review presents summarized data
on the effect of impaired microRNA biogenesis on long-term memory formation, including those associated with
sleep deprivation. In addition, analysis is provided of the current literature related to the prospects of improving
cognitive processes by influencing microRNA biogenesis via the use of CRISPR/Cas9 technologies and active
mental and physical exercises.
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Affiliation(s)
- L. N. Grinkevich
- Pavlov Institute of Physiology of the Russian Academy of Sciences
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Competing Endogenous RNA Networks as Biomarkers in Neurodegenerative Diseases. Int J Mol Sci 2020; 21:ijms21249582. [PMID: 33339180 PMCID: PMC7765627 DOI: 10.3390/ijms21249582] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022] Open
Abstract
Protein aggregation is classically considered the main cause of neuronal death in neurodegenerative diseases (NDDs). However, increasing evidence suggests that alteration of RNA metabolism is a key factor in the etiopathogenesis of these complex disorders. Non-coding RNAs are the major contributor to the human transcriptome and are particularly abundant in the central nervous system, where they have been proposed to be involved in the onset and development of NDDs. Interestingly, some ncRNAs (such as lncRNAs, circRNAs and pseudogenes) share a common functionality in their ability to regulate gene expression by modulating miRNAs in a phenomenon known as the competing endogenous RNA mechanism. Moreover, ncRNAs are found in body fluids where their presence and concentration could serve as potential non-invasive biomarkers of NDDs. In this review, we summarize the ceRNA networks described in Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis and spinocerebellar ataxia type 7, and discuss their potential as biomarkers of these NDDs. Although numerous studies have been carried out, further research is needed to validate these complex interactions between RNAs and the alterations in RNA editing that could provide specific ceRNET profiles for neurodegenerative disorders, paving the way to a better understanding of these diseases.
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Garofalo M, Pandini C, Bordoni M, Pansarasa O, Rey F, Costa A, Minafra B, Diamanti L, Zucca S, Carelli S, Cereda C, Gagliardi S. Alzheimer's, Parkinson's Disease and Amyotrophic Lateral Sclerosis Gene Expression Patterns Divergence Reveals Different Grade of RNA Metabolism Involvement. Int J Mol Sci 2020; 21:ijms21249500. [PMID: 33327559 PMCID: PMC7765024 DOI: 10.3390/ijms21249500] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/27/2020] [Accepted: 12/06/2020] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) are neurodegenerative disorders characterized by a progressive degeneration of the central or peripheral nervous systems. A central role of the RNA metabolism has emerged in these diseases, concerning mRNAs processing and non-coding RNAs biogenesis. We aimed to identify possible common grounds or differences in the dysregulated pathways of AD, PD, and ALS. To do so, we performed RNA-seq analysis to investigate the deregulation of both coding and long non-coding RNAs (lncRNAs) in ALS, AD, and PD patients and controls (CTRL) in peripheral blood mononuclear cells (PBMCs). A total of 293 differentially expressed (DE) lncRNAs and 87 mRNAs were found in ALS patients. In AD patients a total of 23 DE genes emerged, 19 protein coding genes and four lncRNAs. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses, we found common affected pathways and biological processes in ALS and AD. In PD patients only five genes were found to be DE. Our data brought to light the importance of lncRNAs and mRNAs regulation in three principal neurodegenerative disorders, offering starting points for new investigations on deregulated pathogenic mechanisms.
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Affiliation(s)
- Maria Garofalo
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Cecilia Pandini
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
| | - Matteo Bordoni
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy;
| | - Orietta Pansarasa
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
| | - Federica Rey
- Department of Biomedical and Clinical Sciences “Luigi Sacco”, University of Milan, Via G.B Grassi 74, 20157 Milan, Italy; (F.R.); (S.C.)
- Pediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milano, Via G.B. Grassi 74, 20157 Milano, Italy
| | - Alfredo Costa
- Unit of Behavioral Neurology, IRCCS Mondino Foundation, 27100 Pavia, Italy;
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Brigida Minafra
- Parkinson Unit and Movement disorders Mondino Foundation IRCCS, 27100 Pavia, Italy;
| | - Luca Diamanti
- Neuro-Oncology Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy;
| | - Susanna Zucca
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
- enGenomesrl, 27100 Pavia, Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences “Luigi Sacco”, University of Milan, Via G.B Grassi 74, 20157 Milan, Italy; (F.R.); (S.C.)
- Pediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milano, Via G.B. Grassi 74, 20157 Milano, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
- Correspondence:
| | - Stella Gagliardi
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
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Turcotte MA, Garant JM, Cossette-Roberge H, Perreault JP. Guanine Nucleotide-Binding Protein-Like 1 (GNL1) binds RNA G-quadruplex structures in genes associated with Parkinson's disease. RNA Biol 2020; 18:1339-1353. [PMID: 33305682 PMCID: PMC8354592 DOI: 10.1080/15476286.2020.1847866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNAs are highly regulated at the post-transcriptional level in neurodegenerative diseases and just a few mutations can significantly affect the fate of neuronal cells. To date, the impact of G-quadruplex (G4) regulation in neurodegenerative diseases like Parkinson’s disease (PD) has not been analysed. In this study, in silico potential G4s located in deregulated genes related to the nervous system were initially identified and were found to be significantly enriched. Several G4 sequences found in the 5ʹ untranslated regions (5ʹUTR) of mRNAs associated with Parkinson’s disease were demonstrated to in fact fold in vitro by biochemical assays. Subcloning of the full-length 5ʹUTRs of these candidates upstream of a luciferase reporter system led to the demonstration that the G4s of both Parkin RBR E3 Ubiquitin Protein Ligase (PRKN) and Vacuolar Protein Sorting-Associated Protein 35 (VPS35) significantly repressed the translation of both genes in SH-SY5Y cells. Subsequently, a strategy of using label-free RNA affinity purification assays with either of these two G4 sequences as bait isolated the Guanine Nucleotide-Binding Protein-Like 1 (GNL1). The latter was shown to have a higher affinity for the G4 sequences than for their mutated version. This study sheds light on new RNA G-quadruplexes located in genes dysregulated in Parkinson disease and a new G4-binding protein, GNL1.
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Affiliation(s)
- Marc-Antoine Turcotte
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Michel Garant
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Hélène Cossette-Roberge
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Mahernia S, Sarvari S, Fatahi Y, Amanlou M. The Role of HSA21 Encoded Mirna in Down Syndrome Pathophysiology:Opportunities in miRNA-Targeted Pharmacotherapy and Diagnosis of the Down Syndrome. PHARMACEUTICAL SCIENCES 2020. [DOI: 10.34172/ps.2020.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Trisomy 21 is the most prevalent aneuploidy disorder among live-born children worldwide. Itresults from the presence of an extra copy of chromosome 21 which leads to a wide spectrum ofpathophysiological abnormalities and intellectual disabilities. Nevertheless human chromosome21 (HSA21) possess protein non-coding regions where HAS-21 derived-microRNA genes aretranscribed from. In turn, these HSA21-derived miRNAs curb protein translation of severalgenes which are essential to meet memory and cognitive abilities. From the genetics andmolecular biology standpoints, dissecting the mechanistic relationship between DS pathology/symptoms and five chromosome 21-encoded miRNAs including miR-99a, let-7c, miR-125b-2,miR-155 and miR-802 seems pivotal for unraveling novel therapeutic targets. Recently,several studies have successfully carried out small molecule inhibition of miRNAs function,maturation, and biogenesis. One might assume in the case of DS trisomy, the pharmacologicalinhibition of these five overexpressed miRNAs might open new avenues for amelioration of theDS symptoms and complications. In this review, we primarily elucidated the role of HSA21-encoded miRNAs in the DS pathology which in turn introduced and addressed importanttherapeutic targets. Moreover, we reviewed relevant pharmaceutical efforts that based theirgoals on inhibition of these pathological miRNAs at their different biogenesis steps. We havealso discussed the challenges that undermine and question the reliability of miRNAs as noneinvasivebiomarkers in prenatal diagnosis.
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Affiliation(s)
- Shabnam Mahernia
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Sajad Sarvari
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Yousef Fatahi
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Pharmaceutical Nanotechnology, Tehran University of Medical Sciences, Tehran, Iran
| | - Massoud Amanlou
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences,Tehran, Iran
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49
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APOE4 exacerbates synapse loss and neurodegeneration in Alzheimer's disease patient iPSC-derived cerebral organoids. Nat Commun 2020; 11:5540. [PMID: 33139712 PMCID: PMC7608683 DOI: 10.1038/s41467-020-19264-0] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 10/02/2020] [Indexed: 12/25/2022] Open
Abstract
APOE4 is the strongest genetic risk factor associated with late-onset Alzheimer’s disease (AD). To address the underlying mechanism, we develop cerebral organoid models using induced pluripotent stem cells (iPSCs) with APOE ε3/ε3 or ε4/ε4 genotype from individuals with either normal cognition or AD dementia. Cerebral organoids from AD patients carrying APOE ε4/ε4 show greater apoptosis and decreased synaptic integrity. While AD patient-derived cerebral organoids have increased levels of Aβ and phosphorylated tau compared to healthy subject-derived cerebral organoids, APOE4 exacerbates tau pathology in both healthy subject-derived and AD patient-derived organoids. Transcriptomics analysis by RNA-sequencing reveals that cerebral organoids from AD patients are associated with an enhancement of stress granules and disrupted RNA metabolism. Importantly, isogenic conversion of APOE4 to APOE3 attenuates the APOE4-related phenotypes in cerebral organoids from AD patients. Together, our study using human iPSC-organoids recapitulates APOE4-related phenotypes and suggests APOE4-related degenerative pathways contributing to AD pathogenesis. APOE4 is a strong genetic risk factor for late-onset Alzheimer’s disease. Here, the authors show that APOE4 is associated with AD features in hiPSCs-derived cerebral organoids. Isogenic conversion of APOE4 to APOE3 attenuates the AD-associated phenotype.
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50
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Watanabe R, Higashi S, Nonaka T, Kawakami I, Oshima K, Niizato K, Akiyama H, Yoshida M, Hasegawa M, Arai T. Intracellular dynamics of Ataxin-2 in the human brains with normal and frontotemporal lobar degeneration with TDP-43 inclusions. Acta Neuropathol Commun 2020; 8:176. [PMID: 33115537 PMCID: PMC7594343 DOI: 10.1186/s40478-020-01055-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/10/2020] [Indexed: 12/15/2022] Open
Abstract
TAR DNA-binding protein of 43 kDa (TDP-43) is a major component of intracellular aggregates formed in brains of the patients with frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS), which are correctively referred to as TDP-43 proteinopathies. A link between Ataxin-2 (ATXN2) and TDP-43 proteinopathies was established when intermediate CAG repeat expansions of ATXN2 gene were found to be associated with ALS and it was shown that ATXN2 modifies TDP-43 toxicity. Although ATXN2's contribution to TDP-43 proteinopathies has been mostly studied in ALS, recent studies have shown that intermediate repeat expansions of ATXN2 also influence the phenotype of FTLD by an unknown mechanism. To address this issue, we immunohistochemically and biochemically analyzed the intracellular dynamics of ATXN2 in brains of normal controls and FTLD-TDP cases. The immunohistochemical studies revealed that ATXN2 localized in the neuronal cytoplasm and proximal dendrites, and expressed widely and uniformly in normal human brains. A semi-quantitative immunofluorescent analysis of normal brains revealed that the cytoplasmic ATXN2 strongly associates with ribosomal protein S6 and poly-A binding protein 1 and partially overlaps with the endoplasmic reticulum marker Calnexin, suggesting a major role of ATXN2 in protein synthesis. The results of immunohistochemical and biochemical analyses of brains from FTLD-TDP cases showed the colocalization of ATXN2 and phosphorylated TDP-43 in the dystrophic neurites and the neuronal cytoplasmic inclusions in the hippocampal region, and a significant reduction of ATXN2 protein compared to controls. These results suggest that ATXN2 is involved in the pathological process of FTLD-TDP. It remains to be clarified whether reduced ATXN2 expression induces neurodegeneration by impairing protein synthesis or plays a neuroprotective role by attenuating the toxicity of TDP-43 aggregates in FTLD-TDP and other TDP-43 proteinopathies.
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Affiliation(s)
- Ryohei Watanabe
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo Japan
- Department of Psychiatry, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, 2-1-1 Kamikitazawa, Setagaya, Tokyo Japan
| | - Shinji Higashi
- Department of Psychiatry, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki Japan
- Department of Psychiatry, Tokyo Medical University Ibaraki Medical Center, 3-20-1 Chuo, Ami, Inashiki, Ibaraki Japan
| | - Takashi Nonaka
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo Japan
| | - Ito Kawakami
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, 2-1-1 Kamikitazawa, Setagaya, Tokyo Japan
- Brain Bank for Aging Research, Department of Neuropathology, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakaecho, Itabashi, Tokyo Japan
| | - Kenichi Oshima
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, 2-1-1 Kamikitazawa, Setagaya, Tokyo Japan
| | - Kazuhiro Niizato
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, 2-1-1 Kamikitazawa, Setagaya, Tokyo Japan
| | - Haruhiko Akiyama
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo Japan
- Department of Clinical Research, Yokohama Brain and Spine Center, 1-2-1 Takigashira, Isogo, Yokohama, Kanagawa Japan
| | - Mari Yoshida
- Institute for Medical Science of Aging, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi Japan
| | - Masato Hasegawa
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo Japan
| | - Tetsuaki Arai
- Department of Psychiatry, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki Japan
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